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Chlorine in PDB 5lce: Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide

Enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide, PDB code: 5lce was solved by A.Sandner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.39 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.873, 71.200, 72.636, 90.00, 100.44, 90.00
R / Rfree (%) 14 / 16.8

Other elements in 5lce:

The structure of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide (pdb code 5lce). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide, PDB code: 5lce:

Chlorine binding site 1 out of 1 in 5lce

Go back to Chlorine Binding Sites List in 5lce
Chlorine binding site 1 out of 1 in the Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Thrombin in Complex with (S)-1-((R)-2-Amino-3-Cyclohexylpropanoyl)-N- (5-Chloro-2-(Hydroxymethyl)Benzy L)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl301

b:14.8
occ:1.00
 CL H:6TH301 0.0 14.8 1.0
C17 H:6TH301 1.7 14.6 1.0
C16 H:6TH301 2.7 14.5 1.0
C18 H:6TH301 2.7 16.0 1.0
O H:TRP215 3.4 13.8 1.0
O H:PHE227 3.4 12.7 1.0
N H:PHE227 3.6 12.6 1.0
CA H:GLY226 3.7 13.9 1.0
CG1 H:VAL213 3.8 13.6 1.0
N H:TRP215 3.9 12.7 1.0
CB H:ALA190 3.9 16.3 1.0
C H:TRP215 3.9 13.8 1.0
C H:GLY226 4.0 12.1 1.0
C19 H:6TH301 4.0 16.2 1.0
C15 H:6TH301 4.0 14.6 1.0
N H:SER214 4.0 11.9 1.0
CZ H:TYR228 4.0 13.0 1.0
OH H:TYR228 4.1 14.2 1.0
C H:PHE227 4.2 11.4 1.0
CE1 H:TYR228 4.3 13.2 1.0
CE2 H:TYR228 4.3 13.6 1.0
CA H:TRP215 4.4 13.1 1.0
C H:SER214 4.5 12.8 1.0
C20 H:6TH301 4.5 16.3 1.0
CA H:PHE227 4.5 11.9 1.0
OD1 H:ASP189 4.5 16.7 1.0
CA H:VAL213 4.6 11.1 1.0
N H:GLY216 4.6 13.9 1.0
C H:VAL213 4.7 11.5 1.0
CB H:VAL213 4.7 12.1 1.0
O H:HOH467 4.8 15.9 1.0
CD2 H:TYR228 4.8 11.9 1.0
CD1 H:TYR228 4.8 12.6 1.0
CA H:SER214 4.8 12.2 1.0
O H:GLY226 5.0 13.1 1.0
CA H:ALA190 5.0 15.3 1.0

Reference:

A.Sandner, T.Hufner-Wulsdorf, A.Heine, T.Steinmetzer, G.Klebe. Strategies For Late-Stage Optimization: Profiling Thermodynamics By Preorganization and Salt Bridge Shielding. J.Med.Chem. V. 62 9753 2019.
ISSN: ISSN 0022-2623
PubMed: 31633354
DOI: 10.1021/ACS.JMEDCHEM.9B01196
Page generated: Fri Jul 26 11:19:09 2024

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